Switch phylo and alignment dependencies back

lafita · lafita · commit 45a66c7a80e8 · 2015-11-17T17:21:23.000+01:00
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
@@ -62,6 +62,11 @@
   		<dependency>
     		<groupId>org.apache.logging.log4j</groupId>
     		<artifactId>log4j-core</artifactId>
-  		</dependency>			
+  		</dependency>
+  		<dependency>
+  			<groupId>org.biojava</groupId>
+  			<artifactId>biojava-phylo</artifactId>
+  			<version>4.1.1-SNAPSHOT</version>
+  		</dependency>
 	</dependencies>
 </project>
diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml
@@ -59,10 +59,5 @@
     		<groupId>org.apache.logging.log4j</groupId>
     		<artifactId>log4j-core</artifactId>
   		</dependency>
-  		<dependency>
-  			<groupId>org.biojava</groupId>
-  			<artifactId>biojava-alignment</artifactId>
-  			<version>4.1.1-SNAPSHOT</version>
-  		</dependency>
   </dependencies>
 </project>
diff --git a/biojava-phylo/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java b/biojava-phylo/src/main/java/org/biojava/nbio/phylo/ForesterWrapper.java
@@ -9,7 +9,6 @@
 import org.biojava.nbio.core.sequence.template.Compound;
 import org.biojava.nbio.core.sequence.template.Sequence;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
-import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.io.parsers.FastaParser;
 import org.forester.io.writers.PhylogenyWriter;
 import org.forester.msa.Msa;
@@ -26,7 +25,8 @@
 public class ForesterWrapper {
 
 	/** Prevent instantiation */
-	private ForesterWrapper() {}
+	private ForesterWrapper() {
+	}
 
 	/**
 	 * Convert a BioJava {@link MultipleSequenceAlignment} to a forester
@@ -79,21 +79,24 @@ public static String getNewickString(Phylogeny phylo, boolean simpleNewick,
 				writeDistances);
 		return newickString.toString();
 	}
-	
+
 	/**
-	 * Helper function to clone a forester DistanceMatrix.
+	 * Helper function to clone a forester symmetrical DistanceMatrix.
 	 * 
-	 * @param distM forester DistanceMatrix
-	 * @return identical copy of the forester DistanceMatrix
+	 * @param distM
+	 *            forester symmetrical DistanceMatrix
+	 * @return identical copy of the forester symmetrical DistanceMatrix
 	 */
-	public static DistanceMatrix cloneDM(DistanceMatrix distM) {
-		
+	public static BasicSymmetricalDistanceMatrix cloneDM(
+			BasicSymmetricalDistanceMatrix distM) {
+
 		int n = distM.getSize();
-		DistanceMatrix cloneDM = new BasicSymmetricalDistanceMatrix(n);
-		
+		BasicSymmetricalDistanceMatrix cloneDM = 
+				new BasicSymmetricalDistanceMatrix(n);
+
 		for (int i = 0; i < n; i++) {
 			cloneDM.setIdentifier(i, distM.getIdentifier(i));
-			for (int j = 0; j < n; j++) {
+			for (int j = i + 1; j < n; j++) {
 				cloneDM.setValue(i, j, distM.getValue(i, j));
 			}
 		}
